Secrets in Stark Tower
by thewriterstory
Summary: This story starts somewhere near the end of the battle with the Chituari, when the team heads to Stark Tower in search of Loki. It is supposed to be Tony-centric and may or not be one-shot. Might be messy because of the flashback. Will be continued if only requested. No warnings in mind. No slash/pairings. Includes: Jarvis and Tony (friendship)


**_Movie-Verse. Starts from the last scenes at Stark tower where Loki is seen on the floor. After they say don't move or something along that line. NO SLASH._**

**_Disclaimer: Don't own anything._**

**_A little inspiration from Oceanbreeze7's 'Understanding'._**

The Avengers - Tony in his Mark VII (Mark 7 prototype) armour without the face plate, Thor with his full strength, Big Jolly Green Beast ready to smash, Clint ready to shoot any arrow, Natasha holding her guns and Captain Spangles holding his Shield - are all in the Stark Tower aiming at Loki.

The SHIELD quinjets arrived; agents from one of them take Loki away and restrain him. The others are provided medical attention. Well, Bruce (who just transformed) and the Asgardian were unscathed. Clint had sharp glass cuts, Natasha had a bleeding wound on her forehead, Steve had a nasty bruise at his side... and Tony! He got the worst!

While the medics/agents were attending to the other Avengers, Tony muttered something about going to the lab to disassemble the armour. His teammates just nodded in pain.

Tony rushed to his lab carefully ensuring his team or any SHIELD agent doesn't see him in a hurry. He had to manually disassemble the armour painfully and alone because his love, Pepper Potts couldn't help him. Oh my... he hasn't even called her yet to say he's still alive and running. Guess he had to add that to his 'to-do' list.

In his lab, the robotic arms help to remove the armour pieces on his limbs. He was using his hands and tools to remove the pieces near his chest.

"Jarvis, warn me if anything bad happens. Monitor my health status and damages"

"Yes sir"

Tony is slowly unscrewing the chest plate and discovers that his arc reactor's casing is damaged.

"Sir, there is some disturbances in the atmosphere of the lab." Jarvis says. There is a strange smell leaking into the room.

"Jarvis, do me a favor and solve the problem yourself. I need a new arc reactor prep pronto. Dummy standby and prove yourself to be helpful."

The little robot chirped pointing to the fire extinguisher.

Yes, for the lack of a better option, you're still on fire safety." Tony Stark tried to please Dummy.

Unknown to him, some chemical from his armor started leaking...

* * *

Upstairs, the team had been fixed up so the agents were leaving. They knew Stark won't come for treatment so they headed back to base. The team started wandering around and admire some precious antiques while surveying the damages around the tower.

"What's taking Tony so long to come back?"

"He might have something urgent to do in his lab." Bruce answered.

"What exactly?" Steve asked curiously.

"Don't ask me. I never came here before." Before Bruce could continue a mini explosion was heard from the lab. The Avengers were taken aback and they gathered near each other.

"Jarvis, what's going on!" Clint asked worriedly.

"Mr. Stark needs medical attention. I'll provide you directions to his lab. Please hurry and get him outside the lab once you're there."

The team went to the lab which Jarvis unlocked and saw that it was half destroyed. The armour was shattered and pieces all over the place while. Tony was against a wall and holding his reactor in his hand. He was out and Clint gently moved him out while Natasha and Bruce wrecked through the already-damaged lab top find a replacement reactor.

Dummy responded to override commands from Jarvis. It helped to find and give them the spare reactor.

"Jarvis, call Ms. Potts now!" Natasha hollered.

Jarvis rang Pepper

After a few rings, Pepper picked up, thinking Tony was calling her.

"Hello! Tony is that you? Are you alive? Speak Tony!" Pepper babbled in fright from one end. She was still on the flight and the buzzing from her end could be heard.

"Ms Potts, Tony is alive and returned safely. But there was an accident in the lab and we need to get a new reactor in him. Please, we need you to teach us how."

Pepper tried explaining instructions but it was too complicated for them to follow. Then she had an idea which... might be dangerour.

"Jarvis, show them the recording when he did it himself." Pepper ordered, with a little hesitation.

"Do you mean when he first started out?" Jarvis asked while loading said recording.

"Yes that one." She whispered in a hushed tone.

"What video?" Everyone except the female assassin seemed curious.

The Avengers crowded around the unconscious Tony as a blue digital screen with a recording appeared.

**| IRON MAN MOVIE 1 shortened SCENE|**

**Tony is gasping, trying to make it to the ground, a heartbeat is loud in his ears as he drops. Crawling and pushing aside a rolling device as he is now ghostly pale, breathe stuttering. **The Avenger notice that the whole in his chest is just like how he was now.

**He reaches for the Arc inside of the glass case Pepper gave him earlier in the movie, but falls short, lying there dying.**

**A hum is heard as Dummy lowers it to his height.**

**"Good Boy" Tony breaths, voice rasp as he lifts it, slamming it onto the ground.**

**Then Tony takes the reactor and inserts it into himself.** Jarvis pauses when necessary so that Bruce can insert the reactor correctly.

"Jarvis, is Tony well now?" Bruce asked.

"Yes, sir. The video is still running, you should continue watching." Jarvis replied.

**Tony still looks deathly pale. Then he takes slow and steady breaths.**

**TONY! TONY?! ARE YOU THERE? Rhodey shouts' were heard.**

**Rhodey sees Tony on the ground and rushes over.**

**"Tony! You okay?"**

**Rhodey rolls over Tony, seeing the Arc glowing in his chest.**

**"Where's Pepper?" Tony groans, grabbing his arm and looking drunk and whoozy because of the bloodshot colour of his eyes.**

**"She's fine. She's with five agents. They're about to arrest Obadiah."**

**"That's not going to be enough."**

* * *

PRESENT: Tony doesn't wake for another few more minutes. They move him to the living room and set him on the couch. They sit in silence and stare into space. They all are devastated. Clint becomes very curious about the video and what happened to Tony.

He asks "Jarvis, can you play the video for us. Whatever happened at that time when Tony became like that… Please?"

The others glare at him angrily.

"What? I'm only trying to find out more to help him!" Clint says in defense.

"Very well, sir. As long as you try not to change your perspective about Mr. Stark and _the hero he is_." Jarvis replied with a little, anger?

The recording of Obadiah and Tony starts playing.

**Tony's living room.**

**He walks in, about to sit on the couch until he hears a phone go off. He takes it, seeing caller I.D. and sits down, flicking the on button to answer Pepper.**

**A loud high pitch noise causes him to stiffen and not say anything**

"Where'd he get that?" Bruce says in a choked voice, other sounds of outrage and agony from the others as Tony gasps for air.

**"Tony? Tony, are you there? Hello?"** **Pepper frantically asks.**

**He falls back, limp and growing pale, eyes bugging out as he is limp, not able to say anything.**

Thor growls. "No warrior deserves to be treated like this!"

**"Breathe. Easy, easy. You remember this one, right?"****Obadiah holds up the sonic device.**

"This is more painful fire him than the World war II battles for me" Steve muttered sourly.

**"It's a shame the government didn't approve it. There's so many applications for causing short-term paralysis. Tony. When I ordered the hit on you, I worried that I was.." ****He pulls out a metal device, the perfect size for the arc reactor**

"Gosh what's that thing?" Steve asked, alarmed as the others watched, deathly pale and color drained from their faces.

**"Killing the golden goose. But, you see, it was just fate that you survived that."**

Tony recoils as his Arc reactor is yanked painfully out of his chest, showing the empty cavity. Tony say's nothing, still paralyzed and unable to stop him from probably dying**.**

"He'll die soon without that device! You idiot! I'll kill you when all this is over!" Clint screams, Natasha tried cooling him down.

**"You had one last golden egg to give. Do you really think that just because you have an idea, it belongs to you? Your father, he helped give us the atomic bomb. Now, what kind of world would it be today if he was as selfish as you? Oh, it's beautiful. Tony, this is your Ninth Symphony. What a masterpiece. Look at that."**

**Obadiah observes, turning the Arc Reactor just in front of Tony.**

**"This is your legacy."**

**"A new generation of weapons with this at its heart. Weapons that will help steer the world back on course, put the balance of power in our hands. The right hands. I wish you could've seen my prototype."**

**Obadiah stated, opening a briefcase and gently placing the Arc Reaction inside it.**

**"It's not as...Well, not as conservative as yours. Too bad you had to involve Pepper** **in this."**

"Leave her out of this, or you'll be sorry" Bruce growled, his eues turned greenish for a short moment.

**"I would have preferred that she lived."**

**Obadiah walks out, leaving Tony on the couch.**

"Where were we during all of this?" Clint muttered and Natasha sighed.

"That undercover and infiltration mission remember?" She snapped, and Clint grumbled under his breath.

**Next scene**

**Tony is gasping, trying to make it to the ground, a heartbeat is loud in his ears as he drops. Crawling and pushing aside a rolling device as he is now ghostly pale, breathe stuttering.**

**"Oh- oh my god." Steve whispers, room turning to watch in morbid fascination, wanting to look away but cant.**

**He reaches for the Arc inside of the glass case Pepper gave him, but falls short, lying there dying.**

**"Reach! Reach you damn idiot!"**

**A hum is heard as Dummy lowers it to his height.**

**"Good Boy" Tony breaths, voice rasp as he lifts it, slamming it onto the ground.**

"…Okay- I really wished we didn't take that mission."

"I wish I wasn't in the ice."

"I was in India and all this happened..."

**Scene change, Tony's lab.**

**Machines work and Tony is in his suit.**

**"That's the coolest thing I've ever seen. Not bad, huh? Let's do it." Rhodey smiled at his genius friend.**

**Tony looks to Rhodey, completely suited up.**

**"You need me to do anything else?"**

**"Keep the skies clear."**

**"Damn!"**

**Rhodey looks to the other suits on the wall and smiled a bigger smile.**

**"Next time, baby." And he sets off to who knows where.**

**Tony is blaring through the sky, looking for Pepper.**

**"How do you think the Mark One chest piece is going to hold up?"**

**"The suit's at 48% power and falling, sir. That chest piece was never designed for sustained flight."**

**"Keep me posted."**

**"It's odd how Tony can communicate with Jarvis like that." Bruce sighed.**

**"Pepper!"**

**Tony calls through a phone.**

**"Tony! Tony, are you okay?"**

**"I'm fine. How are..."**

**"Obadiah, he's gone insane!"**

**"I know. Listen, you'd better get out of there."**

**"He built a suit."**

**_The ground cracks, and Stane rises out of the ground, causing Tony to gasp._**

**"Get out of there right now!'**

**"Where do you think you're going?" Obadiah spotted Pepper.**

**Obadiah laughs, looming over her in a huge silver metallic suit, similar to Tony's but more bulky.**

**"Your services are no longer required."**

**" Pepper!"**

**"Get him!"**

**Tony blasts down, slamming Obadiah into the ground. Tony rises and Obadiah spins, grabbing a car with a screaming family.**

**"There's kids in there!"**

**"Stane!"**

**"I love this suit!"**

**" Put them down!"**

**"Collateral damage, Tony."**

**"Divert power to chest RT. Power reduced to 19%."**

**A beam blasts Obadiah away, the car lands and the terrified woman floors it, running and slamming into Tony, as he scrambles for a hold.**

**"Lady! No, no no no no!" ****He yelps, slipping and having the car drive over him.**

**He groans, getting to his feet as Obadiah grabs a nearby motorcycle, throwing the driver off and hurling it at Tony before grabbing him, slamming him into the ground.**

**"For 30 years, I've been holding you up! I built this company from nothing!"**

**At each phrase, he flings Tony into the ground.**

**"Nothing is going to stand in my way."**

**Once again throws Tony onto the ground**

**"Least of all you!"**

**Obadiah points, a missile appearing and shooting just as Tony fires his repulsors, shooting into the air, using flight as Obadiah looks up.**

**"Impressive! You've upgraded your armor! I've made some upgrades of my own!"**** Obadiah's suit moves, legs twisting as suddenly, rockets appear and he lifts off, at a much slower pace at first before gaining speed.**

**"Sir, it appears that his suit can fly."**

**"Duly noted. Take me to maximum altitude."**

**"With only 15% power, the odds of reaching that..."**

**"I know the math! Do it!"**

**Scene Change.**

**The air force base, people are looking at the screens in surprise.**

**"Sir, you're not going to believe this. That thing is back."**

**"Get me Major Allen. Scramble the jets!"**

**"Not necessary, people. Just a training exercise." ****Rhodey warns, and the major swallows before nodding, putting down the phone.**

**"Yes, sir."**

**Scene Change**

**Tony is flying while Obadiah is following, they get higher and higher, the city lights fading.**

**"Thirteen percent power, sir."**

** "Climb!"**

**"Eleven percent."**

**"KEEEP GOING!"**

"Oh goodness Tony… What's wrong with you" Clint groans, and they watch as they get higher, Obadiah gaining. Bruce tightens his grip on the nearest object he could find.

**"Seven percent power." Jarvis interrupted Tony again.**

**"Just leave it on the screen! STOP TELLING ME!"**

**Obadiah grabs Tony's neck, not noticing the ice that is coating his suit.**

**"You had a great idea, Tony, but my suit is more advanced in every way!"**

**"Yeah? How'd you solve the icing problem?" ****Tony asks, noticing the ice that covers Obadiah.**

**"Icing problem?"**

**"Might want to look into it." Tony smirks behind the faceplate.**

**Obadiah plummets as a block of ice, Tony following, flailing as the repulsors seem to not work.**

**"Two percent. We are now running on emergency backup power." ****He descends further, jets flickering as he takes a fall then slows himself to descend. He let Obadiah plummet so now he is plummeting.**

**"Potts!"**

**"Tony! Oh, my God, are you okay?" Pepper addresses him informally.**

**Tony lands on the roof of the Main Reactor, stumbling a few steps. ****"I'm almost out of power. I've got to get out of this thing. I'll be right there." ****Tony knocks off one of his gloves, Obadiah landing behind him. He ducks a punch, throwing out a hand of the glove he just discarded, before being grabbed and squished, suit failing slightly.**

**"Fight him!"**

**"Nice try!"**

**"Weapons status?"**

**"Repulsors offline. Missiles offline."**

**"Flares!"**

**A flash of light blinds Obadiah as Tony ducks, leaning against one of the pillars, hiding out of sight.**

**"Very clever, Tony." Obadiah roars.**

**"Potts?"**

**"Tony!"**

**"This isn't working. We're going to have to overload the reactor and blast the roof."**

"Doctor?" The less intelligent heroes look towards Bruce for an explanation when he himself burst out "NO! The backlash energy would override his reactor- he'll kill himself!" The Other Guy was going to make his appearance any time now.

**"Well, how are you going to do that?"**

**"_You're_ going to do it. Go to the central console, open up all the circuits. When I get clear of the roof, I'll let you know. You're going to hit the master bypass button. It's going to fry everything up here."**

**Pepper nods, seeing the broken glass on everything as she walks through the open doorways, walking towards the sparking reactor.**

**"Okay. I'm going in now."**

**"Make sure you wait till I clear the roof. I'll buy you some time." ****Tony whispers before turning and jumping on the back of Obadiah. He tugs, yanking a large wire out from his back.**

**"This looks important!" He says 'jokingly'.**

**Obadiah roars, his sight blinded as he throws off Tony, causing the man to scramble as he nearly falls into the skylight- the glass having shattered. Obadiah opens the main compartment, his targeting systems having broken.**

**"I never had a taste for this sort of thing, but I must admit, I'm deeply enjoying the suit! You finally outdid yourself, Tony! You'd have made your father proud!" ****Obadiah aims and misses several weapons, his targeting system gone and he being a lousy shot.**

**"It's ready, Tony! Get off the roof!"**

**Obadiah sends some blasts towards Tony but misses and hits the roof.**

**"TONY!" ****Pepper screams, crouching as glass from the weapons' impact raining down on her.**

**"How ironic, Tony! Trying to rid the world of weapons, you gave it its best one ever!"**

**He gasps as a missile nearly hits him, causing his grip to loosen.**

**"PEPPER!" He shouts, looking down at the woman far below.**

"How on earth did you survive this Tony?" The teammates all think. Thor seems greatly distressed as he tries to follow the 'moving pictures of Midgard.'

**"And now I'm going to kill you with it! You ripped out my targeting system!"**

**"Time to hit the button!" ****He screams, knowing that everything is futile.**

"No- Don't hit it!" Bruce shouts.

**"You told me not to!"**

**"Hold still, you little prick!" ****More missiles nearly collide with him, causing him to dangle with one arm.**

**"JUST DO IT!" You could hear the desperation his voice.**

**"You'll die!" Pepper had a pleading tone**

"…He- he's going to do it." Steve whispered, flinching. Everyone knew what was to come next."Tony has a thing for suicidal moves." Natasha noted, eyes narrowed.

**"PUSH IT!" Tony's voice cracks.**

**Pepper presses the button, and the Arc flares, Pepper screams, running out of the building as electricity travels upwards.**

**The power rushes up, Tony managing to pull himself up and rolling out of the direct way as Obadiah shouts, electricity frying him and causing his suit to fall down into the core of the Reactor.**

**"Tony!" Pepper screams, voice mirrored by the Avengers. _"Nononononono...please be okay...Tony..."_**

**Fire explodes upwards as Obadiah falls into the main core, shooting high into the sky by where Tony is.**

**The fireworks end and Tony is seen lying on the ground stiff, not moving an inch. His Arc Reactor fizzling as it faintly tries to stat a lit- slowly dying out as the screen moves away.**

The Avenger stared in silence for their fallen warrior.

"What- what just happened?" Steve dares to ask, blinking while the others just stared blankly.

"If I didn't know better, I'd say that he just killed himself." Bruce stated.

Then Jarvis proceeded to play another clip which was from SHIELD,without warning the avengers. It wasn't from the movie and he played so that he could make a certain someone feel guilty…

** "Big man in a suit of armour... take that away what are you?"**

**"Genius, Billionaire, Playboy, Philanthrophist."**

**Natasha smiled and shrugged as if she was impressed and Thor laughed in amusement.**

**"I know guys with none of that worth ten of you. I've seen the footage. The only thing you really fight for is yourself. You're not the guy to make the sacrifice play, to lay down on the wire and let the other guy crawl over you.''**

**"I think I'd just cut the wire."**

**Steve looked at Bruce and smirked.**

**"Always a way out. You know you may not be a threat, but you better stop pretending to be a hero."**

**"A hero? Like you? You're a laboratory experiment, Rogers. Everything special about you came out of a bottle."**

**Rogers stared at him with icy eyes.**

**"Put on the suit. Let's go a few rounds."**

**"Hahaha. You people are so petty, and tiny." Thor chuckled.**

**"Yeah, this is a team," Bruce voiced in the background.**

**The explosion occurred after that.**

"That took a toll on you am I right, Mr Rogers?" Jarvis spoke. Everyone turned to Steve in concern, not anger.

"You should have seen how depressed, how frightened and how scared he came home after that explosion." Jarvis continued; he seemed to have feelings by protecting and defending Mr. Stark behind his back.

A silence.

"I agreed to playing the videos with a purpose, Agent Barton. To get back right at you all. In fact, to be specific, Director Fury, Captain America and Agent Romanoff for degrading my creator. Do not think that I have not been watching your every moves that have affected him so greatly. Even when he was flying the nuke into space you did nothing much or praise him in his dying moments. If you do not know, I tell you now that you have scarred his heart as great as the late Obadiah Stane and Howard."

Everyone looked in different directions guiltily.

"Do not get me mistaken. I am programmed to care for Mr Starks needs. But let me get it clear that you or any SHIELD agent DOES NOT UNDERESTIMATE MR. STARK. Agent Romanoff, you should apologize on behalf of Mr. Fury and yourself for not treating Iron man and Mr. Stark one and the same."

Everyone gulped in shock and astonishment.

"I shall leave you to talk unless you need me to provide you with more evidence. I can gladly clarify any doubts of yours."

"What was that about not treating 'Iron man and Mr. Stark one and the same' Nat?" Clint questioned.

"Fury made me go undercover so that we could evaluate him. He and I were the only two among us who knew about the Avengers initiative before Loki invaded."

"Wait since he knew about it why was he so reluctant to join us? He wanted to do everything alone, not follow orders of his team and boss."

Just then Tony enters the land of the living and looks at his team, at his chest and then the team again. His eyes widened in realization as he realise they had inserted one of his old reactors into him. He catches on the last few sentences and realise they didn't notice him.

"Because she didn't recommend me." Tony said flatly.

"How long have you been awake?" Thor asked.

He shrugged and gave a fake smile. Ignoring the haunting stares of his teammates, Tony excuses himself and slipped out to his lab. He doesn't have time for questions, sensing that something is amiss.

He sees the demolished lab and the memories of the explosion & the chemical leak flood back.

"Jarvis..." Tony growled, irritated with himself, "show me what happened immediately after I was gone."

* * *

A similar blue screen appeared and Tony scanned through important parts of the surveillance video. He didn't see Jarvis reprimanding the Avengers but saw them watching the fight scenes between him and Obadiah.

"What the? YOU SHOWED THEM THAT THING? AND THE WHOLE FIGHT WITH THAT MANIAC? YOU SHOWED OBADIAH?! That WAS A SECRET! YOU SHOWED ALL OF THEM SO THAT THEY COULD RIP MY HEART OUT?" Tony wanted to continue yelling at Jarvis but he clutched his heart in pain.

"Jarvis!" He said as he tapped the arc reactor.

"Sir, this reactor core is made out of palladium."

"Okay, prep my other lab in this tower. The one in the basement. We have work to do."

* * *

Jarvis did as he told.

Tony was briskly walking to the said lab.

A strange feeling overcame him.

_He has flashbacks of Afganistan._

_He sees the weapons presentation, the ride in the jeep,_

_the attack and also the bomb he had made long ago coming towards him._

_He has an open heart surgery and screams in pain and sleeps after the surgery ends._

_He sees himself hooked to car battery and taken into captivity._

_As the Merchant of Death,_

_he refused to comply with the terrorists to make the Jericho missile._

_He is tortured and electrocuted._

_He builds the miniature arc reactor with a box of scraps._

_He sees Yinsen running out of the door trying to buy time for him to suit up._

_He sees the terrorists firing with his weapons._

_He sees Yinsen dying in his arms._

_He sees himself escaping and flying away._

_He sees his armour breaking apart and falls in the desert, resuming his travel by foot._

_He sees a rescue helicopter and falls to his knees._

**Now he is being tortured mentally, letting the nightmares overtake him. **

**He takes one last glance at his surroundings **

**as he nears towards the lab and takes a deep breath. **

**T****he world around him goes dark and there is no one **

**to catch him fall down the stairs near the lab.**

**"Avengers**," Jarvis says sadly, "**Mr. Stark is devastated and doesn't trust you anymore. He thinks you would go to the extent of ripping his reactor out of him-**"

"**just like Obadiah**" Natasha finishes the sentence for him.

* * *

Done! My first Avengers fic. Tony centric. If you want this to be continued, tell me in a PM/review. Or else I'll leave this as a one-shot. Constructive feedback is welcome but flames will burn in your face. Let me know what you feel about this fanfic!


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